2023
Journal article
Open Access
From unstructured texts to semantic story maps
Bartalesi V., Coro G., Lenzi E., Pagano P., Pratelli N.
Digital maps greatly support storytelling about territories, especially when enriched with data describing cultural, societal, and ecological aspects, conveying emotional messages that describe the territory as a whole. Story maps are interactive online digital narratives that can describe a territory beyond its map by enriching the map with text, pictures, videos, and other multimedia information. This paper presents a semi-automatic workflow to produce story maps from textual documents containing territory data. An expert first assembles one territory-contextual document containing text and images. Then, automatic processes use natural language processing and Wikidata services to (i) extract key concepts (entities) and geospatial coordinates associated with the territory, (ii) assemble a logically-ordered sequence of enriched story-map events, and (iii) openly publish online story maps and an interoperable Linked Open Data semantic knowledge base for event exploration and inter-story correlation analyses. Our workflow uses an Open Science-oriented methodology to publish all processes and data. Through our workflow, we produced story maps for the value chains and territories of 23 rural European areas of 16 countries. Through numerical evaluation, we demonstrated that territory experts considered the story maps effective in describing their territories, and appropriate for communicating with citizens and stakeholders.Source: International journal of digital earth (Online) 16 (2023): 234–250. doi:10.1080/17538947.2023.2168774
DOI: 10.1080/17538947.2023.2168774
Project(s): MOVING
Metrics:
Bartalesi V., Coro G., Lenzi E., Pagano P., Pratelli N.
Digital maps greatly support storytelling about territories, especially when enriched with data describing cultural, societal, and ecological aspects, conveying emotional messages that describe the territory as a whole. Story maps are interactive online digital narratives that can describe a territory beyond its map by enriching the map with text, pictures, videos, and other multimedia information. This paper presents a semi-automatic workflow to produce story maps from textual documents containing territory data. An expert first assembles one territory-contextual document containing text and images. Then, automatic processes use natural language processing and Wikidata services to (i) extract key concepts (entities) and geospatial coordinates associated with the territory, (ii) assemble a logically-ordered sequence of enriched story-map events, and (iii) openly publish online story maps and an interoperable Linked Open Data semantic knowledge base for event exploration and inter-story correlation analyses. Our workflow uses an Open Science-oriented methodology to publish all processes and data. Through our workflow, we produced story maps for the value chains and territories of 23 rural European areas of 16 countries. Through numerical evaluation, we demonstrated that territory experts considered the story maps effective in describing their territories, and appropriate for communicating with citizens and stakeholders.Source: International journal of digital earth (Online) 16 (2023): 234–250. doi:10.1080/17538947.2023.2168774
DOI: 10.1080/17538947.2023.2168774
Project(s): MOVING
Metrics:
See at:
ISTI Repository 
| ISTI Repository | www.tandfonline.com | CNR ExploRA
2023
Journal article
Open Access
D4SCIENCE: a unique infrastructure delivering virtual research environments as a service
Candela L., Castelli D., Pagano P.
Nowadays, research challenges - often based on the collaborative analysis of a large amount of data - require suitable infrastructures and user-facing solutions promoting multidisciplinary collaboration and appropriate communication and sharing of data, processes, and outcomes. The D4Science infrastructure and its virtual research environments proved to be a viable and effective solution for many communities of practice and use cases.Source: ERCIM news 133 (2023): 6–7.
Project(s): Blue Cloud, SoBigData-PlusPlus
Candela L., Castelli D., Pagano P.
Nowadays, research challenges - often based on the collaborative analysis of a large amount of data - require suitable infrastructures and user-facing solutions promoting multidisciplinary collaboration and appropriate communication and sharing of data, processes, and outcomes. The D4Science infrastructure and its virtual research environments proved to be a viable and effective solution for many communities of practice and use cases.Source: ERCIM news 133 (2023): 6–7.
Project(s): Blue Cloud
, SoBigData-PlusPlus
See at:
ercim-news.ercim.eu | ISTI Repository | CNR ExploRA
2023
Journal article
Open Access
The D4Science experience on virtual research environment development
Candela L., Castelli D., Pagano P.
Today, complex research challenges, often based on the analysis of a large amount of data, require multidisciplinary collaboration and appropriate communication and sharing of data, processes and outcomes. Technologies and large-scale infrastructures provide stakeholders with computing capacity and data services to perform unprecedented levels of data-driven scientific activities. This opens the way to science gateways and virtual research environments supporting researchers in scientific and educational activities. This article describes our extensive experience with the Virtual Research Environments (VRE) operated by the D4Science infrastructure. It presents how this infrastructure supports their development, their basic functionalities and how they are easily customised to serve the needs of specific user communities. It also describes how they are used in real contexts. The article concludes by reporting how VREs are now progressively used as valuable instruments to support open science and how this role might become more relevant in the future.Source: Computing in science & engineering (Online) 25 (2023). doi:10.1109/MCSE.2023.3290433
DOI: 10.1109/mcse.2023.3290433
Project(s): Blue Cloud, EOSC-Pillar , SoBigData-PlusPlus
Metrics:
Candela L., Castelli D., Pagano P.
Today, complex research challenges, often based on the analysis of a large amount of data, require multidisciplinary collaboration and appropriate communication and sharing of data, processes and outcomes. Technologies and large-scale infrastructures provide stakeholders with computing capacity and data services to perform unprecedented levels of data-driven scientific activities. This opens the way to science gateways and virtual research environments supporting researchers in scientific and educational activities. This article describes our extensive experience with the Virtual Research Environments (VRE) operated by the D4Science infrastructure. It presents how this infrastructure supports their development, their basic functionalities and how they are easily customised to serve the needs of specific user communities. It also describes how they are used in real contexts. The article concludes by reporting how VREs are now progressively used as valuable instruments to support open science and how this role might become more relevant in the future.Source: Computing in science & engineering (Online) 25 (2023). doi:10.1109/MCSE.2023.3290433
DOI: 10.1109/mcse.2023.3290433
Project(s): Blue Cloud
, EOSC-Pillar , SoBigData-PlusPlus Metrics:
See at:
ISTI Repository | ieeexplore.ieee.org 
| CNR ExploRA
2023
Journal article
Open Access
ARIADNE Plus e il D4GNA-Dataset per il Geoportale Nazionale per l'Archeologia
Acconcia V., Boi V., Candela L., Falcone A., Mangiacrapa F., Massara F., Pagano P., Sinibaldi F.
L'articolo racconta l'esperienza del D4GNA - Dataset per il Geoportale Nazionale dell'Archeologia nato nell'ambito del progetto ARIADNEplus (Advanced Research Infrastructure for Archaeological Dataset Networking in Europe - plus), conclusosi lo scorso 31 dicembre. Il contributo parte dal contesto più ampio del progetto europeo per addentrarsi nel mondo dei dati archeologici italiani; la soluzione tecnologica, la standardizzazione, la dematerializzazione e la condivisione in rete dei dati sono i temi toccati in questo percorso che ci illustra il procedere verso un obiettivo virtuoso: il Geoportale Nazionale per l'Archeologia (GNA). Il GNA, realizzato dall'Istituto Centrale per l'Archeologia (ICA) e che sarà in rete dal 10 luglio 2023, è il punto di accesso nazionale per accogliere e consultare gli interventi archeologici svolti sotto la direzione scientifica del Ministero della Cultura (MiC), le indagini archeologiche condotte da università e altri enti di ricerca, nonché altre banche dati territoriali.Source: Digitalia (Online) 1 (2023): 129–140. doi:10.36181/digitalia-00064
DOI: 10.36181/digitalia-00064
Project(s): ARIADNEplus
Metrics:
Acconcia V., Boi V., Candela L., Falcone A., Mangiacrapa F., Massara F., Pagano P., Sinibaldi F.
L'articolo racconta l'esperienza del D4GNA - Dataset per il Geoportale Nazionale dell'Archeologia nato nell'ambito del progetto ARIADNEplus (Advanced Research Infrastructure for Archaeological Dataset Networking in Europe - plus), conclusosi lo scorso 31 dicembre. Il contributo parte dal contesto più ampio del progetto europeo per addentrarsi nel mondo dei dati archeologici italiani; la soluzione tecnologica, la standardizzazione, la dematerializzazione e la condivisione in rete dei dati sono i temi toccati in questo percorso che ci illustra il procedere verso un obiettivo virtuoso: il Geoportale Nazionale per l'Archeologia (GNA). Il GNA, realizzato dall'Istituto Centrale per l'Archeologia (ICA) e che sarà in rete dal 10 luglio 2023, è il punto di accesso nazionale per accogliere e consultare gli interventi archeologici svolti sotto la direzione scientifica del Ministero della Cultura (MiC), le indagini archeologiche condotte da università e altri enti di ricerca, nonché altre banche dati territoriali.Source: Digitalia (Online) 1 (2023): 129–140. doi:10.36181/digitalia-00064
DOI: 10.36181/digitalia-00064
Project(s): ARIADNEplus
Metrics:
See at:
digitalia.cultura.gov.it | ISTI Repository | CNR ExploRA
2023
Contribution to conference
Open Access
Towards digital twins of territories through semantic story maps
Bartalesi V., Coro G., Lenzi E., Pratelli N., Pagano P.
Digital maps greatly support storytelling about territories, especially when enriched with data describing cultural, societal, and ecological aspects, conveying emotional messages that describe the territory as a whole. Story maps are interactive online digital narratives that can describe a territory beyond its map by enriching the map with text, pictures, videos, and other multimedia information. This paper outlines how online story maps can fill the gap between a map and a territory in narratives to create a digital twin of different territories as inter-connected semantic storiesSource: BUILD-IT 2023, pp. 41–45, Rome, Italy, 19/10/2023-20/10/2023
Bartalesi V., Coro G., Lenzi E., Pratelli N., Pagano P.
Digital maps greatly support storytelling about territories, especially when enriched with data describing cultural, societal, and ecological aspects, conveying emotional messages that describe the territory as a whole. Story maps are interactive online digital narratives that can describe a territory beyond its map by enriching the map with text, pictures, videos, and other multimedia information. This paper outlines how online story maps can fill the gap between a map and a territory in narratives to create a digital twin of different territories as inter-connected semantic storiesSource: BUILD-IT 2023, pp. 41–45, Rome, Italy, 19/10/2023-20/10/2023
See at:
inm.cnr.it | ISTI Repository | CNR ExploRA
2023
Journal article
Open Access
Using semantic story maps to describe a territory beyond its map
Bartalesi V., Coro G., Lenzi E., Pratelli N., Pagano P., Felici F., Moretti M., Brunori G.
The paper presents the Story Map Building and Visualizing Tool (SMBVT) that allows users to create story maps within a collaborative environment and a usable Web interface. It is entirely open-source and published as a free-to-use solution. It uses Semantic Web technologies in the back-end system to represent stories through a reference ontology for representing narratives. It builds up a user-shared semantic knowledge base that automatically interconnects all stories and seamlessly enables collaborative story building. Finally, it operates within an Open-Science oriented e-Infrastructure, which enables data and information sharing within communities of narrators, and adds multi-tenancy, multi-user, security, and access-control facilities. SMBVT represents narratives as a network of spatiotemporal events related by semantic relations and standardizes the event descriptions by assigning internationalized resource identifiers (IRIs) to the event components, i.e., the entities that take part in the event (e.g., persons, objects, places, concepts). The tool automatically saves the collected knowledge as a Web Ontology Language (OWL) graph and openly publishes it as Linked Open Data. This feature allows connecting the story events to other knowledge bases. To evaluate and demonstrate our tool, we used it to describe the Apuan Alps territory in Tuscany (Italy). Based on a user-test evaluation, we assessed the tool's effectiveness at building story maps and the ability of the produced story to describe the territory beyond the map.Source: Semantic web (Online) (2023). doi:10.3233/SW-233485
DOI: 10.3233/sw-233485
Metrics:
Bartalesi V., Coro G., Lenzi E., Pratelli N., Pagano P., Felici F., Moretti M., Brunori G.
The paper presents the Story Map Building and Visualizing Tool (SMBVT) that allows users to create story maps within a collaborative environment and a usable Web interface. It is entirely open-source and published as a free-to-use solution. It uses Semantic Web technologies in the back-end system to represent stories through a reference ontology for representing narratives. It builds up a user-shared semantic knowledge base that automatically interconnects all stories and seamlessly enables collaborative story building. Finally, it operates within an Open-Science oriented e-Infrastructure, which enables data and information sharing within communities of narrators, and adds multi-tenancy, multi-user, security, and access-control facilities. SMBVT represents narratives as a network of spatiotemporal events related by semantic relations and standardizes the event descriptions by assigning internationalized resource identifiers (IRIs) to the event components, i.e., the entities that take part in the event (e.g., persons, objects, places, concepts). The tool automatically saves the collected knowledge as a Web Ontology Language (OWL) graph and openly publishes it as Linked Open Data. This feature allows connecting the story events to other knowledge bases. To evaluate and demonstrate our tool, we used it to describe the Apuan Alps territory in Tuscany (Italy). Based on a user-test evaluation, we assessed the tool's effectiveness at building story maps and the ability of the produced story to describe the territory beyond the map.Source: Semantic web (Online) (2023). doi:10.3233/SW-233485
DOI: 10.3233/sw-233485
Metrics:
See at:
content.iospress.com | ISTI Repository | CNR ExploRA
2022
Journal article
Open Access
Virtual research environments co-creation: the D4Science experience
Assante M., Candela L., Castelli D., Cirillo R., Coro G., Dell'Amico A., Frosini L., Lelii L., Lettere M., Mangiacrapa F., Pagano P., Panichi G., Piccioli T., Sinibaldi F.
Virtual research environments are systems called to serve the needs of their designated communities of practice. Every community of practice is a group of people dynamically aggregated by the willingness to collaborate to address a given research question. The virtual research environment provides its users with seamless access to the resources of interest (namely, data and services) no matter what and where they are. Developing a virtual research environment thus to guarantee its uptake from the community of practice is a challenging task. In this article, we advocate how the co-creation driven approach promoted by D4Science has proven to be effective. In particular, we present the co-creation options supported, discuss how diverse communities of practice have exploited these options, and give some usage indicators on the created VREs.Source: Concurrency and computation (Online) (2022). doi:10.1002/cpe.6925
DOI: 10.1002/cpe.6925
Project(s): AGINFRA PLUS, Blue Cloud , EOSC-Pillar , SoBigData-PlusPlus
Metrics:
Assante M., Candela L., Castelli D., Cirillo R., Coro G., Dell'Amico A., Frosini L., Lelii L., Lettere M., Mangiacrapa F., Pagano P., Panichi G., Piccioli T., Sinibaldi F.
Virtual research environments are systems called to serve the needs of their designated communities of practice. Every community of practice is a group of people dynamically aggregated by the willingness to collaborate to address a given research question. The virtual research environment provides its users with seamless access to the resources of interest (namely, data and services) no matter what and where they are. Developing a virtual research environment thus to guarantee its uptake from the community of practice is a challenging task. In this article, we advocate how the co-creation driven approach promoted by D4Science has proven to be effective. In particular, we present the co-creation options supported, discuss how diverse communities of practice have exploited these options, and give some usage indicators on the created VREs.Source: Concurrency and computation (Online) (2022). doi:10.1002/cpe.6925
DOI: 10.1002/cpe.6925
Project(s): AGINFRA PLUS
, Blue Cloud , EOSC-Pillar , SoBigData-PlusPlus Metrics:
See at:
ISTI Repository | onlinelibrary.wiley.com | CNR ExploRA
2022
Software
Unknown
Story Map Building and Visualising Tool (SMBVT)
Lenzi E., Bartalesi V., Pratelli N., Coro G., Pagano P.
In the context of the MOVING (MOuntain Valorisation through INterconnectedness and Green growth) project, we released an open-source software - the MOVING Story Map Building and Visualization Tool (SMBVT) - that allows users to create and visualise story maps within a collaborative environment and using a user-friendly Web interface. The tool uses Semantic Web technologies and the Narrative Ontology to represent the stories of the MOVING mountain Value Chains. The MOVING community access SMBVT through The MOVING story map Virtual Research Environment and creates the events of the story. For each event, the user can add: a title, a textual description, start and end dates, the geographic coordinates, a media object (i.e. a video or image), notes, and digital objects. The tool takes Wikidata as reference KB and assigns Wikidata Internationalized Resource Identifiers (IRIs) to the story components (i.e. the entities that take part in an event). All the knowledge collected by SMBVT is stored in a JSON Postgres DB. When a story is completed, the tool automatically creates the corresponding visualisation using StoryMapJS library and makes available a corresponding URL that can be freely shared. Finally, SMBVT saves the collected knowledge as a Web Ontology Language (OWL) graph and publishes it as a Linked Open Data.Project(s): "CMG Collaborative Research": A Systematic Approach to Large Amplitude Internal Wave Dynamics: An Integrated Mathematical, Observational, and Remote Sensing Model, Blue Cloud, MOVING
Lenzi E., Bartalesi V., Pratelli N., Coro G., Pagano P.
In the context of the MOVING (MOuntain Valorisation through INterconnectedness and Green growth) project, we released an open-source software - the MOVING Story Map Building and Visualization Tool (SMBVT) - that allows users to create and visualise story maps within a collaborative environment and using a user-friendly Web interface. The tool uses Semantic Web technologies and the Narrative Ontology to represent the stories of the MOVING mountain Value Chains. The MOVING community access SMBVT through The MOVING story map Virtual Research Environment and creates the events of the story. For each event, the user can add: a title, a textual description, start and end dates, the geographic coordinates, a media object (i.e. a video or image), notes, and digital objects. The tool takes Wikidata as reference KB and assigns Wikidata Internationalized Resource Identifiers (IRIs) to the story components (i.e. the entities that take part in an event). All the knowledge collected by SMBVT is stored in a JSON Postgres DB. When a story is completed, the tool automatically creates the corresponding visualisation using StoryMapJS library and makes available a corresponding URL that can be freely shared. Finally, SMBVT saves the collected knowledge as a Web Ontology Language (OWL) graph and publishes it as a Linked Open Data.Project(s): "CMG Collaborative Research": A Systematic Approach to Large Amplitude Internal Wave Dynamics: An Integrated Mathematical, Observational, and Remote Sensing Model, Blue Cloud
, MOVING See at: github.com | CNR ExploRA
2022
Dataset
Unknown
Virtual research environments ethnography: a preliminary study
Arezoumandan M., Candela L., Castelli D., Ghannadrad A., Mangione D., Pagano P.
This dataset is accompanying the paper "Virtual Research Environments Ethnography: a Preliminary Study" paper published at 14th International Workshop on Science Gateways 15th-17th June 2022, Trento, Italy. This is a systematic mapping study on the literature about Science gateways, Virtual Research Environments, and Virtual Laboratories.DOI: 10.5281/zenodo.6481183
Project(s): Blue Cloud, EOSC-Pillar , DESIRA , SoBigData-PlusPlus
Metrics:
Arezoumandan M., Candela L., Castelli D., Ghannadrad A., Mangione D., Pagano P.
This dataset is accompanying the paper "Virtual Research Environments Ethnography: a Preliminary Study" paper published at 14th International Workshop on Science Gateways 15th-17th June 2022, Trento, Italy. This is a systematic mapping study on the literature about Science gateways, Virtual Research Environments, and Virtual Laboratories.DOI: 10.5281/zenodo.6481183
Project(s): Blue Cloud
, EOSC-Pillar , DESIRA , SoBigData-PlusPlus Metrics:
See at: CNR ExploRA
2022
Conference article
Open Access
Data models for an imaging bio-bank for colorectal, prostate and gastric cancer: the NAVIGATOR project
Berti A., Carloni G., Colantonio S., Pascali M. A., Manghi P., Pagano P., Buongiorno R., Pachetti E., Caudai C., Di Gangi D., Carlini E., Falaschi Z., Ciarrocchi E., Neri E., Bertelli E., Miele V., Carpi R., Bagnacci G., Di Meglio N., Mazzei M. A., Barucci A.
Researchers nowadays may take advantage of broad collections of medical data to develop personalized medicine solutions. Imaging bio-banks play a fundamental role, in this regard, by serving as organized repositories of medical images associated with imaging biomarkers. In this context, the NAVIGATOR Project aims to advance colorectal, prostate, and gastric oncology translational research by leveraging quantitative imaging and multi-omics analyses. As Project's core, an imaging bio-bank is being designed and implemented in a web-accessible Virtual Research Environment (VRE). The VRE serves to extract the imaging biomarkers and further process them within prediction algorithms. In our work, we present the realization of the data models for the three cancer use-cases of the Project. First, we carried out an extensive requirements analysis to fulfill the necessities of the clinical partners involved in the Project. Then, we designed three separate data models utilizing entity-relationship diagrams. We found diagrams' modeling for colorectal and prostate cancers to be more straightforward, while gastric cancer required a higher level of complexity. Future developments of this work would include designing a common data model following the Observational Medical Outcomes Partnership Standards. Indeed, a common data model would standardize the logical infrastructure of data models and make the bio-bank easily interoperable with other bio-banks.Source: BHI '22 - IEEE-EMBS International Conference on Biomedical and Health Informatics, Ioannina, Greece, 27-30/09/2022
DOI: 10.1109/bhi56158.2022.9926910
Metrics:
Berti A., Carloni G., Colantonio S., Pascali M. A., Manghi P., Pagano P., Buongiorno R., Pachetti E., Caudai C., Di Gangi D., Carlini E., Falaschi Z., Ciarrocchi E., Neri E., Bertelli E., Miele V., Carpi R., Bagnacci G., Di Meglio N., Mazzei M. A., Barucci A.
Researchers nowadays may take advantage of broad collections of medical data to develop personalized medicine solutions. Imaging bio-banks play a fundamental role, in this regard, by serving as organized repositories of medical images associated with imaging biomarkers. In this context, the NAVIGATOR Project aims to advance colorectal, prostate, and gastric oncology translational research by leveraging quantitative imaging and multi-omics analyses. As Project's core, an imaging bio-bank is being designed and implemented in a web-accessible Virtual Research Environment (VRE). The VRE serves to extract the imaging biomarkers and further process them within prediction algorithms. In our work, we present the realization of the data models for the three cancer use-cases of the Project. First, we carried out an extensive requirements analysis to fulfill the necessities of the clinical partners involved in the Project. Then, we designed three separate data models utilizing entity-relationship diagrams. We found diagrams' modeling for colorectal and prostate cancers to be more straightforward, while gastric cancer required a higher level of complexity. Future developments of this work would include designing a common data model following the Observational Medical Outcomes Partnership Standards. Indeed, a common data model would standardize the logical infrastructure of data models and make the bio-bank easily interoperable with other bio-banks.Source: BHI '22 - IEEE-EMBS International Conference on Biomedical and Health Informatics, Ioannina, Greece, 27-30/09/2022
DOI: 10.1109/bhi56158.2022.9926910
Metrics:
See at:
ISTI Repository | ieeexplore.ieee.org | CNR ExploRA
2022
Contribution to conference
Open Access
Blue-Cloud: exploring and demonstrating the potential of Open Science for ocean sustainability
Schaap D., Assante M., Pagano P., Candela L.
The Blue-Cloud project is part of 'The Future of Seas and Oceans Flagship Initiative' of the European Commission and runs since October 2019. It has established a pilot cyber platform, providing researchers access to multidisciplinary datasets and derived data products from observations, in-situ and satellite-based, analytical services, and computing facilities essential for blue science to better understand and manage the many aspects of ocean sustainability. A number of core services have been delivered and are now in a phase of wider dissemination and uptake by marine researchers. Core services are the Federated Data Discovery & Access Service (DD&AS), the Blue-Cloud Virtual Research Environment (VRE), and five Blue-Cloud Virtual Labs.Source: MetroSEA 2022 - IEEE International Workshop on Metrology for the Sea, Milazzo, Italy, 3-5/10/2022
DOI: 10.5281/zenodo.7143580
Project(s): Blue Cloud
Metrics:
Schaap D., Assante M., Pagano P., Candela L.
The Blue-Cloud project is part of 'The Future of Seas and Oceans Flagship Initiative' of the European Commission and runs since October 2019. It has established a pilot cyber platform, providing researchers access to multidisciplinary datasets and derived data products from observations, in-situ and satellite-based, analytical services, and computing facilities essential for blue science to better understand and manage the many aspects of ocean sustainability. A number of core services have been delivered and are now in a phase of wider dissemination and uptake by marine researchers. Core services are the Federated Data Discovery & Access Service (DD&AS), the Blue-Cloud Virtual Research Environment (VRE), and five Blue-Cloud Virtual Labs.Source: MetroSEA 2022 - IEEE International Workshop on Metrology for the Sea, Milazzo, Italy, 3-5/10/2022
DOI: 10.5281/zenodo.7143580
Project(s): Blue Cloud
Metrics:
See at:
ISTI Repository | zenodo.org | CNR ExploRA
2022
Conference article
Open Access
Blue-Cloud: exploring and demonstrating the potential of Open Science for ocean sustainability
Schaap D., Assante M., Pagano P., Candela L.
The Blue-Cloud project is part of 'The Future of Seas and Oceans Flagship Initiative' of the European Commission and runs since October 2019. It has established a pilot cyber platform, providing researchers access to multidisciplinary datasets and derived data products from observations, in-situ and satellite-based, analytical services, and computing facilities essential for blue science to better understand and manage the many aspects of ocean sustainability. A number of core services have been delivered and are now in a phase of wider dissemination and uptake by marine researchers. Core services are the Federated Data Discovery & Access Service (DD&AS), the Blue-Cloud Virtual Research Environment (VRE), and five Blue-Cloud Virtual Labs.Source: MetroSEA 2022 - IEEE International Workshop on Metrology for the Sea, pp. 198–202, Milazzo, Italy, 3-5/10/2022
DOI: 10.1109/metrosea55331.2022.9950819
Project(s): Blue Cloud
Metrics:
Schaap D., Assante M., Pagano P., Candela L.
The Blue-Cloud project is part of 'The Future of Seas and Oceans Flagship Initiative' of the European Commission and runs since October 2019. It has established a pilot cyber platform, providing researchers access to multidisciplinary datasets and derived data products from observations, in-situ and satellite-based, analytical services, and computing facilities essential for blue science to better understand and manage the many aspects of ocean sustainability. A number of core services have been delivered and are now in a phase of wider dissemination and uptake by marine researchers. Core services are the Federated Data Discovery & Access Service (DD&AS), the Blue-Cloud Virtual Research Environment (VRE), and five Blue-Cloud Virtual Labs.Source: MetroSEA 2022 - IEEE International Workshop on Metrology for the Sea, pp. 198–202, Milazzo, Italy, 3-5/10/2022
DOI: 10.1109/metrosea55331.2022.9950819
Project(s): Blue Cloud
Metrics:
See at:
ISTI Repository | ieeexplore.ieee.org | CNR ExploRA
2022
Report
Unknown
MOVING D3.3 - Tools for science-society-policy interfaces. Using semantic story maps to describe a territory beyond its map
Bartalesi V., Coro G., Lenzi E., Pratelli N., Pagano P.
Maps have always stimulated people's imagination and spatiotemporally supported storytelling; however, they cannot alone represent the life and emotions associated with the territories they describe. Story maps are an IT solution to enrich maps with such information. They are online applications enriched with multimedia and textual information that tell map-based stories. Current software for story map building is either commercial or requires advanced IT skills that make it hardly used by environmental experts. This deliverable describes the Story Map Building and Visualizing Tool (SBVMT), an open-source and free-to-use tool to build and publish story maps, which overcomes common drawbacks of other software by operating within the open-science e-Infrastructure (D4Science) used in the MOVING Project. SBVMT includes new features such as an ontology to represent story maps, Semantic Web technologies for data representation, automatic connection to Wikidata, secure multi-user collaboration in story building, and visualisation of the narrative either as a story map or a timeline. This deliverable shows how SBVMT can overcome the perceptual gap between territory and map. We evaluated its usability and effectiveness from both the point of view of experts building the story map and users interacting with it. Using SMBVT we created the story maps related to the MOVING selected regions. Furthermore, exploiting the semantic web technologies, we implemented several SPARQL queries that allow linking different stories and discovering new knowledge.Source: ISTI Research Report, MOVING, D3.3, 2022
Project(s): MOVING
Bartalesi V., Coro G., Lenzi E., Pratelli N., Pagano P.
Maps have always stimulated people's imagination and spatiotemporally supported storytelling; however, they cannot alone represent the life and emotions associated with the territories they describe. Story maps are an IT solution to enrich maps with such information. They are online applications enriched with multimedia and textual information that tell map-based stories. Current software for story map building is either commercial or requires advanced IT skills that make it hardly used by environmental experts. This deliverable describes the Story Map Building and Visualizing Tool (SBVMT), an open-source and free-to-use tool to build and publish story maps, which overcomes common drawbacks of other software by operating within the open-science e-Infrastructure (D4Science) used in the MOVING Project. SBVMT includes new features such as an ontology to represent story maps, Semantic Web technologies for data representation, automatic connection to Wikidata, secure multi-user collaboration in story building, and visualisation of the narrative either as a story map or a timeline. This deliverable shows how SBVMT can overcome the perceptual gap between territory and map. We evaluated its usability and effectiveness from both the point of view of experts building the story map and users interacting with it. Using SMBVT we created the story maps related to the MOVING selected regions. Furthermore, exploiting the semantic web technologies, we implemented several SPARQL queries that allow linking different stories and discovering new knowledge.Source: ISTI Research Report, MOVING, D3.3, 2022
Project(s): MOVING
See at: CNR ExploRA
2022
Report
Open Access
InfraScience research activity report 2021
Artini M., Assante M., Atzori C., Baglioni M., Bardi A., Bove P., Candela L., Casini G., Castelli D., Cirillo R., Coro G., De Bonis M., Debole F., Dell'Amico A., Frosini L., La Bruzzo S., Lazzeri E., Lelii L., Manghi P., Mangiacrapa F., Mangione D., Mannocci A., Ottonello E., Pagano P., Panichi G., Pavone G., Piccioli T., Sinibaldi F., Straccia U.
InfraScience is a research group of the National Research Council of Italy - Institute of Information Science and Technologies (CNR - ISTI) based in Pisa, Italy. This report documents the research activity performed by this group in 2021 to highlight the major results. In particular, the InfraScience group confronted with research challenges characterising Data Infrastructures, eScience, and Intelligent Systems. The group activity is pursued by closely connecting research and development and by promoting and supporting open science. In fact, the group is leading the development of two large scale infrastructures for Open Science, i.e. D4Science and OpenAIRE. During 2021 InfraScience members contributed to the publishing of 25 papers, to the research and development activities of 18 research projects (15 funded by EU), to the organization of conferences and training events, to several working groups and task forces.Source: ISTI Annual report, 2022
DOI: 10.32079/isti-ar-2022/001
Project(s): ARIADNEplus, Blue Cloud , PerformFISH , EOSC-Pillar , DESIRA , EOSC Future , EOSCsecretariat.eu , EcoScope , RISIS 2 , OpenAIRE-Advance , OpenAIRE Nexus , SoBigData-PlusPlus
Metrics:
Artini M., Assante M., Atzori C., Baglioni M., Bardi A., Bove P., Candela L., Casini G., Castelli D., Cirillo R., Coro G., De Bonis M., Debole F., Dell'Amico A., Frosini L., La Bruzzo S., Lazzeri E., Lelii L., Manghi P., Mangiacrapa F., Mangione D., Mannocci A., Ottonello E., Pagano P., Panichi G., Pavone G., Piccioli T., Sinibaldi F., Straccia U.
InfraScience is a research group of the National Research Council of Italy - Institute of Information Science and Technologies (CNR - ISTI) based in Pisa, Italy. This report documents the research activity performed by this group in 2021 to highlight the major results. In particular, the InfraScience group confronted with research challenges characterising Data Infrastructures, eScience, and Intelligent Systems. The group activity is pursued by closely connecting research and development and by promoting and supporting open science. In fact, the group is leading the development of two large scale infrastructures for Open Science, i.e. D4Science and OpenAIRE. During 2021 InfraScience members contributed to the publishing of 25 papers, to the research and development activities of 18 research projects (15 funded by EU), to the organization of conferences and training events, to several working groups and task forces.Source: ISTI Annual report, 2022
DOI: 10.32079/isti-ar-2022/001
Project(s): ARIADNEplus
, Blue Cloud , PerformFISH , EOSC-Pillar , DESIRA , EOSC Future , EOSCsecretariat.eu , EcoScope , RISIS 2 , OpenAIRE-Advance , OpenAIRE Nexus , SoBigData-PlusPlus Metrics:
See at:
ISTI Repository | CNR ExploRA
2022
Journal article
Open Access
NAVIGATOR: an Italian regional imaging biobank to promote precision medicine for oncologic patients
Borgheresi R., Barucci A., Colantonio S., Aghakhanyan G., Assante M., Bertelli E., Carlini E., Carpi R., Caudai C., Cavallero D., Cioni D., Cirillo R., Colcelli V., Dell'Amico A., Di Gangi D., Erba P. A., Faggioni L., Falaschi Z., Gabelloni M., Gini R., Lelii L., Liò P., Lorito A., Lucarini S., Manghi P., Mangiacrapa F., Marzi C., Mazzei M. A., Mercatelli L., Mirabile A., Mungai F., Miele V., Olmastroni M., Pagano P., Paiar F., Panichi G., Pascali M. A., Pasquinelli F., Shortrede J. E., Tumminello L., Volterrani L., Neri E., On Behalf Of The Navigator Consortium Group
NAVIGATOR is an Italian regional project to boost precision medicine in oncology with the aim to make it more predictive, preventive, and personalised by advancing translational research based on quantitative imaging and integrative omics analyses. The project's goal is to develop an open imaging biobank for the collection and preservation of a large amount of standardised imaging multimodal datasets, including computed tomography, magnetic resonance imaging, and positron emission tomography data, together with the corresponding patient-related and omics-related relevant information extracted from regional healthcare services using an adapted privacy-preserving model. The project is based on an open-source imaging biobank and an open-science oriented virtual research environment (VRE). Available integrative omics and multi-imaging data of three use cases (prostate cancer, rectal cancer, and gastric cancer) will be collected. All data confined in NAVIGATOR (i.e. standard and novel imaging biomarkers, non-imaging data, health agency data) will be used to create a digital patient model, to support the reliable prediction of the disease phenotype and risk stratification. The VRE that relies on a well-established infrastructure, called D4Science.org, will further provide a multiset infrastructure for processing the integrative omics data, extracting specific radiomic signatures, and for identification and testing of novel imaging biomarkers through big data analytics and artificial intelligence.Source: European radiology experimental Online 6 (2022). doi:10.1186/s41747-022-00306-9
DOI: 10.1186/s41747-022-00306-9
Metrics:
Borgheresi R., Barucci A., Colantonio S., Aghakhanyan G., Assante M., Bertelli E., Carlini E., Carpi R., Caudai C., Cavallero D., Cioni D., Cirillo R., Colcelli V., Dell'Amico A., Di Gangi D., Erba P. A., Faggioni L., Falaschi Z., Gabelloni M., Gini R., Lelii L., Liò P., Lorito A., Lucarini S., Manghi P., Mangiacrapa F., Marzi C., Mazzei M. A., Mercatelli L., Mirabile A., Mungai F., Miele V., Olmastroni M., Pagano P., Paiar F., Panichi G., Pascali M. A., Pasquinelli F., Shortrede J. E., Tumminello L., Volterrani L., Neri E., On Behalf Of The Navigator Consortium Group
NAVIGATOR is an Italian regional project to boost precision medicine in oncology with the aim to make it more predictive, preventive, and personalised by advancing translational research based on quantitative imaging and integrative omics analyses. The project's goal is to develop an open imaging biobank for the collection and preservation of a large amount of standardised imaging multimodal datasets, including computed tomography, magnetic resonance imaging, and positron emission tomography data, together with the corresponding patient-related and omics-related relevant information extracted from regional healthcare services using an adapted privacy-preserving model. The project is based on an open-source imaging biobank and an open-science oriented virtual research environment (VRE). Available integrative omics and multi-imaging data of three use cases (prostate cancer, rectal cancer, and gastric cancer) will be collected. All data confined in NAVIGATOR (i.e. standard and novel imaging biomarkers, non-imaging data, health agency data) will be used to create a digital patient model, to support the reliable prediction of the disease phenotype and risk stratification. The VRE that relies on a well-established infrastructure, called D4Science.org, will further provide a multiset infrastructure for processing the integrative omics data, extracting specific radiomic signatures, and for identification and testing of novel imaging biomarkers through big data analytics and artificial intelligence.Source: European radiology experimental Online 6 (2022). doi:10.1186/s41747-022-00306-9
DOI: 10.1186/s41747-022-00306-9
Metrics:
See at:
eurradiolexp.springeropen.com | ISTI Repository | CNR ExploRA
2022
Report
Open Access
Blue-Cloud D4.6 - Blue Cloud VRE Operation Report (Release 2)
M. Assante, L. Candela, P. Pagano, R. Cirillo, A. Dell'Amico, L. Frosini, L. Lelii, F. Mangiacrapa, G. Panichi, F. Sinibaldi
The Blue-Cloud project developed a cyber platform bringing together and providing access to multidisciplinary data from observations and models, analytical tools, and computing facilities essential to support research to better understand and manage the many aspects of ocean sustainability. The Blue-Cloud platform architecture consists of two major families of components: (a) the Blue Cloud Data Discovery and Access service to serve federated discovery and access to 'blue data' infrastructures, and (b) the Blue Cloud Virtual Research Environment (VRE) to provide a Blue Cloud VRE as a federation of computing platforms and analytical services. This Deliverable D4.6 "Blue Cloud VRE Operation (Release 2)" is the revised and updated version of the D4.1 "Blue Cloud VRE Operation (Release 1)" [10]. It reports on the Blue-Cloud Virtual Research Environment (VRE) by complementing the architecture and infrastructure described in [9], where the constituents have been discussed. Specifically, this deliverable focuses on how the components have been exploited and operated to support the development of the Blue-Cloud gateway https://blue-cloud.d4science.org, its underlying infrastructure, and the VLabs. 9 Blue-Cloud VLabs were created and operated in the first period, while an additional 5 Blue-Cloud VLabs were created and operated in the second reporting period, from M17 (February 2021) to M35 (September 2022), bringing the total on 14 operational VLabs. Two VLabs of the second reporting period are specifically conceived to support the developments of the Blue-Cloud Demonstrators: (i) The Plankton Genomics VLab has been developed in the context of the Demonstrator #2, and (ii) The Marine Environmental Indicators Dev VLab has been developed in the context of the Demonstrator #3 - Marine Environmental Indicators. In order to support the Blue-Cloud Hackathon1 event held in February 2022 the (iii) Blue-Cloud Hackathon VLab has been developed. Finally, in the framework of the Blue-Cloud synergies programme two additional VLabs were developed as pilots to support the work of (iv) the JERICO-CORE multi-platform research infrastructure dedicated to a holistic appraisal of coastal marine system changes, and (v) the JONAS initiative, addressing the issue of underwater noise in the Atlantic Seas. These working environments are serving more than 1,300 users in total spread across more than 20 countries. Up to mid of September 2022, a total of more than 25,700 working sessions have been executed, with an average of 1,286 working sessions per month since the start of the Blue-Cloud project in October 2019. A total of more than 2,230 analytics sessions have been executed by the users of the VLabs, with an average of 55 working sessions per month. From M17 (February 2021) to M35 (September 2022), a total of 212 tickets have been created and managed in the Blue-Cloud Project Issue Trackers (85% have been closed). Moreover, 34 tickets related to Blue-Cloud have been created in the D4Science overall context (88% have been closed).Source: ISTI Project report, Blue-Cloud, D4.6, 2022
Project(s): Blue Cloud
M. Assante, L. Candela, P. Pagano, R. Cirillo, A. Dell'Amico, L. Frosini, L. Lelii, F. Mangiacrapa, G. Panichi, F. Sinibaldi
The Blue-Cloud project developed a cyber platform bringing together and providing access to multidisciplinary data from observations and models, analytical tools, and computing facilities essential to support research to better understand and manage the many aspects of ocean sustainability. The Blue-Cloud platform architecture consists of two major families of components: (a) the Blue Cloud Data Discovery and Access service to serve federated discovery and access to 'blue data' infrastructures, and (b) the Blue Cloud Virtual Research Environment (VRE) to provide a Blue Cloud VRE as a federation of computing platforms and analytical services. This Deliverable D4.6 "Blue Cloud VRE Operation (Release 2)" is the revised and updated version of the D4.1 "Blue Cloud VRE Operation (Release 1)" [10]. It reports on the Blue-Cloud Virtual Research Environment (VRE) by complementing the architecture and infrastructure described in [9], where the constituents have been discussed. Specifically, this deliverable focuses on how the components have been exploited and operated to support the development of the Blue-Cloud gateway https://blue-cloud.d4science.org, its underlying infrastructure, and the VLabs. 9 Blue-Cloud VLabs were created and operated in the first period, while an additional 5 Blue-Cloud VLabs were created and operated in the second reporting period, from M17 (February 2021) to M35 (September 2022), bringing the total on 14 operational VLabs. Two VLabs of the second reporting period are specifically conceived to support the developments of the Blue-Cloud Demonstrators: (i) The Plankton Genomics VLab has been developed in the context of the Demonstrator #2, and (ii) The Marine Environmental Indicators Dev VLab has been developed in the context of the Demonstrator #3 - Marine Environmental Indicators. In order to support the Blue-Cloud Hackathon1 event held in February 2022 the (iii) Blue-Cloud Hackathon VLab has been developed. Finally, in the framework of the Blue-Cloud synergies programme two additional VLabs were developed as pilots to support the work of (iv) the JERICO-CORE multi-platform research infrastructure dedicated to a holistic appraisal of coastal marine system changes, and (v) the JONAS initiative, addressing the issue of underwater noise in the Atlantic Seas. These working environments are serving more than 1,300 users in total spread across more than 20 countries. Up to mid of September 2022, a total of more than 25,700 working sessions have been executed, with an average of 1,286 working sessions per month since the start of the Blue-Cloud project in October 2019. A total of more than 2,230 analytics sessions have been executed by the users of the VLabs, with an average of 55 working sessions per month. From M17 (February 2021) to M35 (September 2022), a total of 212 tickets have been created and managed in the Blue-Cloud Project Issue Trackers (85% have been closed). Moreover, 34 tickets related to Blue-Cloud have been created in the D4Science overall context (88% have been closed).Source: ISTI Project report, Blue-Cloud, D4.6, 2022
Project(s): Blue Cloud
See at:
ISTI Repository | CNR ExploRA
2022
Report
Open Access
Blue-Cloud D4.5 - Interfacing EOSC report (Release 2)
Buurman M., Pagano P., Candela L., Widmann H.
The Blue-Cloud Service platform features a variety of services that can be used for undertaking world-class science via the European Open Science Cloud (EOSC) framework, by featuring leading operational marine research infrastructures and e-infrastructures. As part of its service offer, the Blue-Cloud service catalogue gathers all the services enabled in the Blue-Cloud Virtual Research Environment (VRE) that will be onboarded in the EOSC Catalogue. This onboarding, once finished, will allow easy access to all EOSC users to Blue-Cloud services via the EOSC Portal Marketplace. This deliverable describes the onboarding of Blue-Cloud services available in the Blue-Cloud Virtual Research Environment (VRE) into the EOSC Catalogue. It includes details on the activities performed to ensure that the configuration, formats and metadata of resources are compatible with the requirements of the EOSC Catalogue and Marketplace. The document also introduces how providers have been/are being imported and referenced into the EOSC Catalogue and Marketplace. While the different procedures for onboarding 'providers' and 'services' are described in detail in the first release of the deliverable (D4.3), this document goes a step further by describing the actual onboarding within the EOSC Catalogue and should be considered as updated and extended version of D4.3.Source: ISTI Project report, Blue-Cloud, D4.5, 2022
Project(s): Blue Cloud
Buurman M., Pagano P., Candela L., Widmann H.
The Blue-Cloud Service platform features a variety of services that can be used for undertaking world-class science via the European Open Science Cloud (EOSC) framework, by featuring leading operational marine research infrastructures and e-infrastructures. As part of its service offer, the Blue-Cloud service catalogue gathers all the services enabled in the Blue-Cloud Virtual Research Environment (VRE) that will be onboarded in the EOSC Catalogue. This onboarding, once finished, will allow easy access to all EOSC users to Blue-Cloud services via the EOSC Portal Marketplace. This deliverable describes the onboarding of Blue-Cloud services available in the Blue-Cloud Virtual Research Environment (VRE) into the EOSC Catalogue. It includes details on the activities performed to ensure that the configuration, formats and metadata of resources are compatible with the requirements of the EOSC Catalogue and Marketplace. The document also introduces how providers have been/are being imported and referenced into the EOSC Catalogue and Marketplace. While the different procedures for onboarding 'providers' and 'services' are described in detail in the first release of the deliverable (D4.3), this document goes a step further by describing the actual onboarding within the EOSC Catalogue and should be considered as updated and extended version of D4.3.Source: ISTI Project report, Blue-Cloud, D4.5, 2022
Project(s): Blue Cloud
See at:
ISTI Repository | CNR ExploRA
2022
Report
Open Access
Blue-Cloud D2.8 - Blue-Cloud Architecture (Release 3)
Schaap D. M. A., Thijsse P., Pagano P., Assante M., Candela L., Boldrini E., Buurman M., D'Antonio M., Ariyo C., Maudire G., Nys C., Chiavarini B., Lettere M.
This deliverable D2.8 describes third and final release of the Blue-Cloud architecture as it is at Month 33 (June 2022) and it is and an update of the earlier 2nd release of the Blue-Cloud architecture document D2.7. Given the agreed extension allowed to the Blue-Cloud project until March 2023, there might be some further refinements to the architecture in the upcoming 9 months to allow to optimise some of its services to better respond to user needs. In order to make it easier for readers and reviewers, a table is included as part of Chapter 1, which indicates the elements and sections of this Deliverable 2.8, which have been updated or added in comparison with the earlier Deliverable 2.7. In this report, the current architecture and functionalities of each of the following components, part of the Blue-Cloud technical framework, are described in detail as well as the roles of partners that are developing and hosting modules: 1) the Blue-Cloud Data Discovery and Access service to serve federated discovery and access to blue data infrastructures; 2) the Blue-Cloud Virtual Research Environment (VRE) to provide a Blue-Cloud VRE as a federation of computing platforms and analytical services. The Blue-Cloud Data Discovery and Access service architecture is based upon a combination of the DAB metadata broker service of CNR-IIA, and the SeaDataNet CDI service modules as developed by MARIS, IFREMER, and EUDAT in the framework of the EU SeaDataCloud project. For the Blue-Cloud Data Discovery and Access service and its modules, additional developments were implemented in the period May 2021 - June 2022 such as adapting and upgrading existing services, adding new services, testing modules, integrating modules, and testing the integrated service, in order to achieve the planned functionality. The Blue-Cloud VRE is largely based upon the D4Science e-infrastructure as earlier developed and managed by CNR-ISTI [1]. This e-infrastructure hosted, already from the start, multiple Virtual Labs and offered a variety of services. These services have been adopted and adapted for Blue-Cloud, new services have been added and several original services have been upgraded. Moreover, new Virtual Labs have been constructed and deployed as part of the Blue-Cloud Demonstrators. The D4Science e- infrastructure also already included proven solutions for connecting to external computing platforms and means for orchestrating distributed services, which are instrumental for smart connections to the other e-infrastructures in the Blue-Cloud system, while further evolutions have taken place as part of the Blue-Cloud project, in response to the needs of the Virtual Labs and their users. With respect to the Virtual Labs, they are developed as real-life demonstrators embedded in the D4Science VRE and supported by data input from the Blue-Cloud Data Discovery and Access service, other data resources and additional computing services. They have been worked out in cooperation between WP3 and WP4 which have analysed their scientific workflows and identified the best technical set-up considering the D4Science VRE infrastructure and services. As part of their development, the demonstrators required upgrading of existing functionality and development of additional services. This is described, where relevant, in this document. In addition, consideration is given to integration aspects, such as two-way linking between the Blue- Cloud components, expanding the VRE with additional platforms for computing and algorithms, and direct access to data infrastructures where needed for specific Virtual Labs. Moreover, aspects of authentication and monitoring are considered on a full Blue-Cloud scale. The Blue-Cloud architecture as described in this report, is designed to be scalable and sustainable for near-future expansions, such as connecting additional blue data infrastructures, implementing more and advanced blue analytical services, configuring more dedicated Virtual Labs, and targeting more (groups of) users.Source: ISTI Project report, Blue-Cloud, D2.8, 2022
Project(s): Blue Cloud
Schaap D. M. A., Thijsse P., Pagano P., Assante M., Candela L., Boldrini E., Buurman M., D'Antonio M., Ariyo C., Maudire G., Nys C., Chiavarini B., Lettere M.
This deliverable D2.8 describes third and final release of the Blue-Cloud architecture as it is at Month 33 (June 2022) and it is and an update of the earlier 2nd release of the Blue-Cloud architecture document D2.7. Given the agreed extension allowed to the Blue-Cloud project until March 2023, there might be some further refinements to the architecture in the upcoming 9 months to allow to optimise some of its services to better respond to user needs. In order to make it easier for readers and reviewers, a table is included as part of Chapter 1, which indicates the elements and sections of this Deliverable 2.8, which have been updated or added in comparison with the earlier Deliverable 2.7. In this report, the current architecture and functionalities of each of the following components, part of the Blue-Cloud technical framework, are described in detail as well as the roles of partners that are developing and hosting modules: 1) the Blue-Cloud Data Discovery and Access service to serve federated discovery and access to blue data infrastructures; 2) the Blue-Cloud Virtual Research Environment (VRE) to provide a Blue-Cloud VRE as a federation of computing platforms and analytical services. The Blue-Cloud Data Discovery and Access service architecture is based upon a combination of the DAB metadata broker service of CNR-IIA, and the SeaDataNet CDI service modules as developed by MARIS, IFREMER, and EUDAT in the framework of the EU SeaDataCloud project. For the Blue-Cloud Data Discovery and Access service and its modules, additional developments were implemented in the period May 2021 - June 2022 such as adapting and upgrading existing services, adding new services, testing modules, integrating modules, and testing the integrated service, in order to achieve the planned functionality. The Blue-Cloud VRE is largely based upon the D4Science e-infrastructure as earlier developed and managed by CNR-ISTI [1]. This e-infrastructure hosted, already from the start, multiple Virtual Labs and offered a variety of services. These services have been adopted and adapted for Blue-Cloud, new services have been added and several original services have been upgraded. Moreover, new Virtual Labs have been constructed and deployed as part of the Blue-Cloud Demonstrators. The D4Science e- infrastructure also already included proven solutions for connecting to external computing platforms and means for orchestrating distributed services, which are instrumental for smart connections to the other e-infrastructures in the Blue-Cloud system, while further evolutions have taken place as part of the Blue-Cloud project, in response to the needs of the Virtual Labs and their users. With respect to the Virtual Labs, they are developed as real-life demonstrators embedded in the D4Science VRE and supported by data input from the Blue-Cloud Data Discovery and Access service, other data resources and additional computing services. They have been worked out in cooperation between WP3 and WP4 which have analysed their scientific workflows and identified the best technical set-up considering the D4Science VRE infrastructure and services. As part of their development, the demonstrators required upgrading of existing functionality and development of additional services. This is described, where relevant, in this document. In addition, consideration is given to integration aspects, such as two-way linking between the Blue- Cloud components, expanding the VRE with additional platforms for computing and algorithms, and direct access to data infrastructures where needed for specific Virtual Labs. Moreover, aspects of authentication and monitoring are considered on a full Blue-Cloud scale. The Blue-Cloud architecture as described in this report, is designed to be scalable and sustainable for near-future expansions, such as connecting additional blue data infrastructures, implementing more and advanced blue analytical services, configuring more dedicated Virtual Labs, and targeting more (groups of) users.Source: ISTI Project report, Blue-Cloud, D2.8, 2022
Project(s): Blue Cloud
See at:
ISTI Repository | CNR ExploRA
2022
Report
Open Access
ARIADNEplus D15.2 - Final report on ARIADNEplus services
Marberg J. F., Bardi A., Vlachidis A., Meghini C., Binding C., Tudhope D., Sinibaldi F., Ponchio F., Mangiacrapa F., Radman-Livaja I., Callieri M., Potenziani M., Lamé M., Assante M., Pagano P., Hermon S., Vassallo V.
This deliverable describes the activities carried out within Work Package 15 (WP15) of the ARIADNEplus project by the different partners and describes the results achieved. The work package consists of several individual tasks and subtasks with the overall goal to develop and provide useful services to archaeologists. This means the work package is by nature heterogeneous with stand-alone tasks and services. Efforts have been made to facilitate collaboration between the individual tasks through joint work package meetings. This has resulted in new cross-task contacts being made, and some sharing of expertise to improve services has been done. A service design template aligning the ARIADNEplus services with the requirements from European Open Science Cloud (EOSC) has been created. In connection with this, the ARIADNEplus AO-CAT ontology has been adapted to the requirements from EOSC Resource Data Model (Task 15.1). The Visual Media Service (Task 15.2.1) has had a new format added, allowing for 2D visualisation of LIDAR data in DEM format. In addition, three other standards have been added: gITF, ThreeJS and IIIF, supporting various functionality in the service. The service has also been adapted to support integration with the ARIADNEplus infrastructure in D4Science. A visual wizard has been defined to guide Visual Media Service users to add hotspots to a 3D scene easily and quickly. This extension, initially implemented in 3DHOP will allow archaeologists to create interactive links from the digital 3D model to the related documentation without writing any source code (Task 15.2.2). Task 15.2.3 reworked the Online 3D Database System for Endangered architectural and archaeological Heritage in the south Eastern MEditerRAnea area (EpHEMERA). EpHEMERA is a service provided by the Cyprus Institute to visualize in 3D archaeological excavations, ancient buildings, and their related documentation. In EpHEMERA, it is possible to visualise, online and through standard web browsers, 3D architectural and archaeological models (classified according to a specific type of risk), query the database system and retrieve metadata attached to each digital object, and extract geometric and morphological information about the Cultural Heritage asset. The visualisation and annotation tool of the TSS project have been ported to the OpenLime library and integrated into the Visual Media Service (Task 15.2.1). An additional layer of SVG annotations have been developed and added to the service. The Annotation service have been used and improved in three different pilot projects. (Task 15.3.2) Various strands of work have been done improving services for text mining and Natural Language Processing (Task 15.4). One of these efforts has been building upon the outcomes of the preceding ARIADNE project. A set of archaeological Named Entity Recognition NLP pipelines were reconfigured and deployed for easier use on the General Architecture for Text Engineering (GATE) cloud. Another effort has been on extracting temporal archaeological information using two different parallel approaches, normalisation and named entity recognition. A Python development platform has been used to unify the various services. A Vocabulary Annotation Tool (Task 15.3.1) was developed using the same platform, as part of Task 15.4. The tool facilitates the locating and tagging of vocabulary terms within free text and outputs suggested subject annotations in a range of formats. The GeoPortal service (Task 15.5) is a new REST service designed to manage complex spatio-temporal documents defined by metadata profiles. It was released as a component of the gCube framework. A prototype using the service was deployed and operated to manage archaeological excavation projects (Task 15.7). Two services for querying the RDF AO-Cat metadata records aggregated by the ARIADNEplus Infrastructure was established (Task 15.6): a full-text index service and a SPARQL endpoint. The full- text index service is based on OpenSearch and supports the needed query functionality of the ARIADNEplus portal. The SPARQL endpoint allows performance of semantic queries on the RDF records within the ARIADNEplus data and knowledge cloud.Source: ISTI Project report, ARIADNEplus, D15.2, 2022
Project(s): ARIADNEplus
Marberg J. F., Bardi A., Vlachidis A., Meghini C., Binding C., Tudhope D., Sinibaldi F., Ponchio F., Mangiacrapa F., Radman-Livaja I., Callieri M., Potenziani M., Lamé M., Assante M., Pagano P., Hermon S., Vassallo V.
This deliverable describes the activities carried out within Work Package 15 (WP15) of the ARIADNEplus project by the different partners and describes the results achieved. The work package consists of several individual tasks and subtasks with the overall goal to develop and provide useful services to archaeologists. This means the work package is by nature heterogeneous with stand-alone tasks and services. Efforts have been made to facilitate collaboration between the individual tasks through joint work package meetings. This has resulted in new cross-task contacts being made, and some sharing of expertise to improve services has been done. A service design template aligning the ARIADNEplus services with the requirements from European Open Science Cloud (EOSC) has been created. In connection with this, the ARIADNEplus AO-CAT ontology has been adapted to the requirements from EOSC Resource Data Model (Task 15.1). The Visual Media Service (Task 15.2.1) has had a new format added, allowing for 2D visualisation of LIDAR data in DEM format. In addition, three other standards have been added: gITF, ThreeJS and IIIF, supporting various functionality in the service. The service has also been adapted to support integration with the ARIADNEplus infrastructure in D4Science. A visual wizard has been defined to guide Visual Media Service users to add hotspots to a 3D scene easily and quickly. This extension, initially implemented in 3DHOP will allow archaeologists to create interactive links from the digital 3D model to the related documentation without writing any source code (Task 15.2.2). Task 15.2.3 reworked the Online 3D Database System for Endangered architectural and archaeological Heritage in the south Eastern MEditerRAnea area (EpHEMERA). EpHEMERA is a service provided by the Cyprus Institute to visualize in 3D archaeological excavations, ancient buildings, and their related documentation. In EpHEMERA, it is possible to visualise, online and through standard web browsers, 3D architectural and archaeological models (classified according to a specific type of risk), query the database system and retrieve metadata attached to each digital object, and extract geometric and morphological information about the Cultural Heritage asset. The visualisation and annotation tool of the TSS project have been ported to the OpenLime library and integrated into the Visual Media Service (Task 15.2.1). An additional layer of SVG annotations have been developed and added to the service. The Annotation service have been used and improved in three different pilot projects. (Task 15.3.2) Various strands of work have been done improving services for text mining and Natural Language Processing (Task 15.4). One of these efforts has been building upon the outcomes of the preceding ARIADNE project. A set of archaeological Named Entity Recognition NLP pipelines were reconfigured and deployed for easier use on the General Architecture for Text Engineering (GATE) cloud. Another effort has been on extracting temporal archaeological information using two different parallel approaches, normalisation and named entity recognition. A Python development platform has been used to unify the various services. A Vocabulary Annotation Tool (Task 15.3.1) was developed using the same platform, as part of Task 15.4. The tool facilitates the locating and tagging of vocabulary terms within free text and outputs suggested subject annotations in a range of formats. The GeoPortal service (Task 15.5) is a new REST service designed to manage complex spatio-temporal documents defined by metadata profiles. It was released as a component of the gCube framework. A prototype using the service was deployed and operated to manage archaeological excavation projects (Task 15.7). Two services for querying the RDF AO-Cat metadata records aggregated by the ARIADNEplus Infrastructure was established (Task 15.6): a full-text index service and a SPARQL endpoint. The full- text index service is based on OpenSearch and supports the needed query functionality of the ARIADNEplus portal. The SPARQL endpoint allows performance of semantic queries on the RDF records within the ARIADNEplus data and knowledge cloud.Source: ISTI Project report, ARIADNEplus, D15.2, 2022
Project(s): ARIADNEplus
See at:
ISTI Repository | CNR ExploRA
2022
Report
Open Access
ARIADNEplus D13.4 - VREs Operation Final Activity Report
Assante M., Cirillo R., Dell'Amico A., Pagano P., Candela L., Frosini L., Lelii L., Mangiacrapa F., Panichi G., Piccioli T., Sinibaldi F.
Virtual Research Environments (VREs) are "systems" specifically conceived to provide their users with a web-based set of facilities (including services, data and computational facilities) to accomplish a set of tasks by dynamically relying on the underlying infrastructure. VREs are among the key products developed and delivered by the ARIADNEplus project to support the target communities and application scenarios in archaeology. The development of VREs is based on three main activities: (i) the development of software artifacts that realise a set of functions (including those needed for accessing certain datasets), (ii) the deployment of these artifacts in an operational infrastructure following the release procedures and tools presented in the deliverable D13.1 "Software Release Procedures and Tools JRA2", and (iii) the final deployment and operation of well-defined Virtual Research Environments by exploiting the facilities offered by the underlying D4Science infrastructure and its services [1]. This deliverable D13.4 - "VREs Operation Final Activity Report'' is the updated version of D13.2 - "VREs Operation Mid-term Activity Report ''. D13.4 documents the last of the above- mentioned three activities - i.e. the exploitation of the services and technologies offered by the underlying infrastructure to serve the needs of defined scenarios - as implemented in the second period, from January 2021 to November 2022 - of the ARIADNEplus project. Specifically, it focuses on how the components have been exploited and operated to support the development of the ARIADNEplus VRE gateway https://ariadne.d4science.org, its underlying infrastructure, and the VREs from M25 (January 2021) to M47 (November 2022). These activities have been carried out within Work Package 13. Specifically in Task 13.1 Infrastructure Operation (JRA2.1) and Task 13.3 VREs Operation (JRA2.3). In addition to the 5 VREs created and operated in the first period, 3 more VREs were created and operated in the second reporting period, for a total of 8 VREs. One VRE of the second reporting period, namely ARIADNEplus Lab (cf. Section 4.6), was created in July 2021 as the virtual laboratory to support developers, researchers, data managers, and data analysts belonging to the archaeological community worldwide. The "Geoportale Nazionale per l'Archeologia (GNA)" VRE (cf. Section 4.7) was created in January 2022, as the evolution of the existing Geoportal Prototype VRE (cf. Section 4.4), which was developed for the integration, validation, harmonization, visualization, and access of archaeological georeferenced datasets collected in Italy. Finally, the Esquiline VRE (cf. Section 4.8) was created in October 2022 for the integration and display of data originating from 19th century excavations and historical cartography in a spatio-temporal database, allowing the reconstruction of the transformation of an urban landscape through the centuries. As of November 2022, the VREs are serving the needs of more than 400 users in total spread across 21 countries and more than 10.000 user sessions. This required to deal with approximately 100 tickets (59 requests for support, 9 requests for incidents and bugs, 9 requests for Virtual Machine or Container creations).Source: ISTI Project report, ARIADNEplus, D13.4, 2022
Project(s): ARIADNEplus
Assante M., Cirillo R., Dell'Amico A., Pagano P., Candela L., Frosini L., Lelii L., Mangiacrapa F., Panichi G., Piccioli T., Sinibaldi F.
Virtual Research Environments (VREs) are "systems" specifically conceived to provide their users with a web-based set of facilities (including services, data and computational facilities) to accomplish a set of tasks by dynamically relying on the underlying infrastructure. VREs are among the key products developed and delivered by the ARIADNEplus project to support the target communities and application scenarios in archaeology. The development of VREs is based on three main activities: (i) the development of software artifacts that realise a set of functions (including those needed for accessing certain datasets), (ii) the deployment of these artifacts in an operational infrastructure following the release procedures and tools presented in the deliverable D13.1 "Software Release Procedures and Tools JRA2", and (iii) the final deployment and operation of well-defined Virtual Research Environments by exploiting the facilities offered by the underlying D4Science infrastructure and its services [1]. This deliverable D13.4 - "VREs Operation Final Activity Report'' is the updated version of D13.2 - "VREs Operation Mid-term Activity Report ''. D13.4 documents the last of the above- mentioned three activities - i.e. the exploitation of the services and technologies offered by the underlying infrastructure to serve the needs of defined scenarios - as implemented in the second period, from January 2021 to November 2022 - of the ARIADNEplus project. Specifically, it focuses on how the components have been exploited and operated to support the development of the ARIADNEplus VRE gateway https://ariadne.d4science.org, its underlying infrastructure, and the VREs from M25 (January 2021) to M47 (November 2022). These activities have been carried out within Work Package 13. Specifically in Task 13.1 Infrastructure Operation (JRA2.1) and Task 13.3 VREs Operation (JRA2.3). In addition to the 5 VREs created and operated in the first period, 3 more VREs were created and operated in the second reporting period, for a total of 8 VREs. One VRE of the second reporting period, namely ARIADNEplus Lab (cf. Section 4.6), was created in July 2021 as the virtual laboratory to support developers, researchers, data managers, and data analysts belonging to the archaeological community worldwide. The "Geoportale Nazionale per l'Archeologia (GNA)" VRE (cf. Section 4.7) was created in January 2022, as the evolution of the existing Geoportal Prototype VRE (cf. Section 4.4), which was developed for the integration, validation, harmonization, visualization, and access of archaeological georeferenced datasets collected in Italy. Finally, the Esquiline VRE (cf. Section 4.8) was created in October 2022 for the integration and display of data originating from 19th century excavations and historical cartography in a spatio-temporal database, allowing the reconstruction of the transformation of an urban landscape through the centuries. As of November 2022, the VREs are serving the needs of more than 400 users in total spread across 21 countries and more than 10.000 user sessions. This required to deal with approximately 100 tickets (59 requests for support, 9 requests for incidents and bugs, 9 requests for Virtual Machine or Container creations).Source: ISTI Project report, ARIADNEplus, D13.4, 2022
Project(s): ARIADNEplus
See at:
ISTI Repository | CNR ExploRA